Wafer based precision glass optics manufacturing has been an innovative approach for combining high accuracy with mass production. However, due to the small ratio of thickness and diameter of the glass wafer, deformation and residual stress would be induced for the nonuniform temperature distribution in the glass wafer after molding. Therefore, thermal modelling of the heating system in the wafer based precision glass molding (PGM) process is of great importance in optimizing the heating system and the technique of the process. The current paper deals with a transient thermal modelling of a self-developed heating system for wafer based PGM process. First, in order to investigate the effect of radiation from the surface and interior of the glass wafer, the thermal modeling is simulated with a discrete ordinates radiation model in the CFD software FLUENT. Temperature distribution of the glass wafer obtained from the simulations is then used to evaluate the performance of heating system and investigate some importance parameters in the model, such as interior and surface radiation in glass wafer, thermal contact conductance between glass wafer and molds, thickness to diameter ratio of glass wafer. Finally, structure modification in the molding chamber is raised to decrease the temperature gradient in the glass wafer and the effect is significant.